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B

backward(ParameterTree[], int[][]) - Method in class de.jstacs.scoringFunctions.directedGraphicalModels.ParameterTree
Computes the backward-part of the normalization constant starting from this ParameterTree.
BayesianNetworkModel - Class in de.jstacs.models.discrete.inhomogeneous
The class implements a Bayesian network ( StructureLearner.ModelType.BN ) of fixed order.
BayesianNetworkModel(BayesianNetworkModelParameterSet) - Constructor for class de.jstacs.models.discrete.inhomogeneous.BayesianNetworkModel
Creates a new BayesianNetworkModel from a given BayesianNetworkModelParameterSet.
BayesianNetworkModel(StringBuffer) - Constructor for class de.jstacs.models.discrete.inhomogeneous.BayesianNetworkModel
The standard constructor for the interface Storable.
BayesianNetworkModelParameterSet - Class in de.jstacs.models.discrete.inhomogeneous.parameters
The ParameterSet for the class BayesianNetworkModel.
BayesianNetworkModelParameterSet(StringBuffer) - Constructor for class de.jstacs.models.discrete.inhomogeneous.parameters.BayesianNetworkModelParameterSet
The standard constructor for the interface Storable.
BayesianNetworkModelParameterSet() - Constructor for class de.jstacs.models.discrete.inhomogeneous.parameters.BayesianNetworkModelParameterSet
The simple constructor for an empty BayesianNetworkModelParameterSet for a BayesianNetworkModel.
BayesianNetworkModelParameterSet(AlphabetContainer, int, double, String, StructureLearner.ModelType, byte, StructureLearner.LearningType) - Constructor for class de.jstacs.models.discrete.inhomogeneous.parameters.BayesianNetworkModelParameterSet
This is the constructor of a filled BayesianNetworkModelParameterSet for a BayesianNetworkModel.
BayesianNetworkScoringFunction - Class in de.jstacs.scoringFunctions.directedGraphicalModels
This class implements a scoring function that is a moral directed graphical model, i.e. a moral Bayesian network.
BayesianNetworkScoringFunction(AlphabetContainer, int, double, boolean, Measure) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.BayesianNetworkScoringFunction
Creates a new BayesianNetworkScoringFunction that has neither been initialized nor trained.
BayesianNetworkScoringFunction(BayesianNetworkScoringFunctionParameterSet) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.BayesianNetworkScoringFunction
Creates a new BayesianNetworkScoringFunction that has neither been initialized nor trained from a BayesianNetworkScoringFunctionParameterSet.
BayesianNetworkScoringFunction(StringBuffer) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.BayesianNetworkScoringFunction
The standard constructor for the interface Storable.
BayesianNetworkScoringFunctionParameterSet - Class in de.jstacs.scoringFunctions.directedGraphicalModels
Class for the parameters of a BayesianNetworkScoringFunction.
BayesianNetworkScoringFunctionParameterSet(AlphabetContainer, int, double, boolean, Measure) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.BayesianNetworkScoringFunctionParameterSet
Creates a new BayesianNetworkScoringFunctionParameterSet with pre-defined parameter values.
BayesianNetworkScoringFunctionParameterSet() - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.BayesianNetworkScoringFunctionParameterSet
Creates a new BayesianNetworkScoringFunctionParameterSet with empty parameter values.
BayesianNetworkScoringFunctionParameterSet(StringBuffer) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.BayesianNetworkScoringFunctionParameterSet
Creates a new BayesianNetworkScoringFunctionParameterSet from its XML representation as defined by the Storable interface.
beta - Variable in class de.jstacs.classifier.scoringFunctionBased.gendismix.GenDisMixClassifier
The weights that determine a point of the simplex that corresponds to the function that is optimized by this classifier.
bgMaxMarkovOrder - Variable in class de.jstacs.models.mixture.motif.SingleHiddenMotifMixture
The order of the background model.
BioJavaAdapter - Class in de.jstacs.data.bioJava
This class provides static methods to convert BioJava datatypes ( SequenceIterator, Sequence) to Samples and vice versa.
BioJavaAdapter() - Constructor for class de.jstacs.data.bioJava.BioJavaAdapter
 
brentsMethod(OneDimensionalFunction, double, double, double, double, double) - Static method in class de.jstacs.algorithms.optimization.Optimizer
Approximates a minimum (not necessary the global) in the interval [lower,upper].
brentsMethod(OneDimensionalFunction, double, double, double, double) - Static method in class de.jstacs.algorithms.optimization.Optimizer
Approximates a minimum (not necessary the global) in the interval [lower,upper].
BTExplainingAwayResidual - Class in de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures
Structure learning Measure that computes a maximum spanning tree based on the explaining away residual and uses the resulting tree structure as structure of a Bayesian tree (special case of a Bayesian network) in a BayesianNetworkScoringFunction .
BTExplainingAwayResidual(double[]) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures.BTExplainingAwayResidual
Creates a new explaining away residual Bayesian tree Measure.
BTExplainingAwayResidual(BTExplainingAwayResidual.BTExplainingAwayResidualParameterSet) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures.BTExplainingAwayResidual
Creates a new BTExplainingAwayResidual from the corresponding InstanceParameterSet parameters.
BTExplainingAwayResidual(StringBuffer) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures.BTExplainingAwayResidual
The standard constructor for the interface Storable.
BTExplainingAwayResidual.BTExplainingAwayResidualParameterSet - Class in de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures
Class for the parameters of a BTExplainingAwayResidual structure Measure.
BTExplainingAwayResidual.BTExplainingAwayResidualParameterSet() - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures.BTExplainingAwayResidual.BTExplainingAwayResidualParameterSet
Creates a new BTExplainingAwayResidual.BTExplainingAwayResidualParameterSet with empty parameter values.
BTExplainingAwayResidual.BTExplainingAwayResidualParameterSet(double[]) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures.BTExplainingAwayResidual.BTExplainingAwayResidualParameterSet
Creates a new BTExplainingAwayResidual.BTExplainingAwayResidualParameterSet with the parameter for the equivalent sample sizes set to ess.
BTExplainingAwayResidual.BTExplainingAwayResidualParameterSet(StringBuffer) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures.BTExplainingAwayResidual.BTExplainingAwayResidualParameterSet
The standard constructor for the interface Storable .
BTMutualInformation - Class in de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures
Structure learning Measure that computes a maximum spanning tree based on mutual information and uses the resulting tree structure as structure of a Bayesian tree (special case of a Bayesian network) in a BayesianNetworkScoringFunction .
BTMutualInformation(StringBuffer) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures.BTMutualInformation
The standard constructor for the interface Storable.
BTMutualInformation(BTMutualInformation.DataSource, double[]) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures.BTMutualInformation
Creates a new mutual information Bayesian tree Measure.
BTMutualInformation(BTMutualInformation.BTMutualInformationParameterSet) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures.BTMutualInformation
Creates a new BTMutualInformation from the corresponding InstanceParameterSet parameters.
BTMutualInformation.BTMutualInformationParameterSet - Class in de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures
Class for the parameters of a BTMutualInformation structure Measure.
BTMutualInformation.BTMutualInformationParameterSet() - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures.BTMutualInformation.BTMutualInformationParameterSet
Creates a new BTMutualInformation.BTMutualInformationParameterSet with empty parameter values.
BTMutualInformation.BTMutualInformationParameterSet(BTMutualInformation.DataSource, double[]) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures.BTMutualInformation.BTMutualInformationParameterSet
Creates a new BTMutualInformation.BTMutualInformationParameterSet with the parameter for the BTMutualInformation.DataSource set to clazz and the parameter for the equivalent sample sizes (ess) set to ess.
BTMutualInformation.BTMutualInformationParameterSet(StringBuffer) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures.BTMutualInformation.BTMutualInformationParameterSet
The standard constructor for the interface Storable .
BTMutualInformation.DataSource - Enum in de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures
Enum defining the possible sources of data to compute the mutual information.
burnInTest - Variable in class de.jstacs.models.mixture.AbstractMixtureModel
The BurnInTest that is used to stop the sampling.
BurnInTest - Class in de.jstacs.models.mixture.gibbssampling
This is the abstract super class for any test of the length of the burn-in phase.
BurnInTest() - Constructor for class de.jstacs.models.mixture.gibbssampling.BurnInTest
 
ByteSequence - Class in de.jstacs.data.sequences
This class is for sequences with the alphabet symbols encoded as bytes and can therefore be used for discrete AlphabetContainers with alphabets that use only few symbols.
ByteSequence(AlphabetContainer, byte[]) - Constructor for class de.jstacs.data.sequences.ByteSequence
Creates a new ByteSequence from an array of byte- encoded alphabet symbols.
ByteSequence(AlphabetContainer, String) - Constructor for class de.jstacs.data.sequences.ByteSequence
Creates a new ByteSequence from a String representation using the default delimiter.
ByteSequence(AlphabetContainer, SequenceAnnotation[], String, String) - Constructor for class de.jstacs.data.sequences.ByteSequence
Creates a new ByteSequence from a String representation using the delimiter delim.
ByteSequence(AlphabetContainer, SequenceAnnotation[], SymbolExtractor) - Constructor for class de.jstacs.data.sequences.ByteSequence
Creates a new ByteSequence from a SymbolExtractor.

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